- Chimera-users - RBVI Mailing Lists

how to know the net charge of my system
by Sara Luz Gomez Maya 29 Jun '21

29 Jun '21

Dear all, I'd like to know if there is a way to know the net charge of a system when opening the pdb file with Chimera. If so, is it possible to do it by means of the command line? Thanks in advance, Sara

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same chain id while saving large coordinate files
by manikandank 27 Jun '21

27 Jun '21

Hi Chimera-users, Chimera 1.15 (build 42258) puts same chain id for all protein chains present in the pdb during 'save pdb/write pdb' . I am using it in linux Ubuntu. Please help. thank you with kind regards Mani.

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Modeller..Waiting for the Opal server
by Hernando J Sosa 26 Jun '21

26 Jun '21

Dear Chimera, Today when trying to use Modeller through the Chimera interface (via web service) the program either stays forever in Waiting for the Opal server or produces a whole bunch of errors. Trying to run Modeller through the local installation also results in errors. Not sure if the problem is with Chimera or Modeller but one day ago Modeller&Chimera were working fine with the same input files that now are causing the errors (???). Thanks Best Hernando

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multi align viewer
by Jacqueline Vitali 25 Jun '21

25 Jun '21

Hi Elaine, When you do match-->align in chimera, you create the MAV. It has a coral region for the fully populated columns. If you change the order of the sequences, it automatically disappears. Is there a way to bring this region back? Thank you. Jackie Vitali Cleveland State University

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multialign viewer
by Jacqueline Vitali 23 Jun '21

23 Jun '21

Hi Elaine, When you do match-->align in chimera, you create the MAV. It has a coral region for the fully populated columns. If you change the order of the sequences, it automatically disappears. Is there a way to bring this region back? Thank you. Jackie Vitali Cleveland State University

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Regarding problem 'During selection from the graphics window (picking)'
by Dr. Abhay Nanda Srivastava 20 Jun '21

20 Jun '21

Dear Team Chimera, I am using Chimera software in Windows 7, 32 bit computer for viewing Swiss dock prediction results. But, when I try to select the residue or atom in model by using mouse and keyboard button (Ctrl+button 1), no selection is displayed, even hand like cursor seen on the graphics, I am also not able to see the residue or atoms labeling by putting cursor on model. For my confusion removal, I have downloaded and installed the software on another computer of Windows 7, 64 bit. But here also, the same problem persists. Please suggest to me, how to get rid of this problem? Looking forward to hearing from you. Thank You. *Regards,* *Dr. Abhay N. Srivastava* * M. Sc. (Chem.), Ph. D. Head & Asst. Professor,* * Department of Chemistry,* * NC-BRA Bihar University,* * Muzaffarpur-India.* * Contact: +91-9990576112*

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Question regarding the chimera Transform Coordinates feature
by Ritwik Jain 19 Jun '21

19 Jun '21

Respected developers of chimera, I am currently doing a research project related to Cryo-EM map alignment in which I need to use Chimera. Chimera has a feature which transforms the coordinates of a molecule (Img1.jpg) . That feature has an option to move atoms instead of coordinate axes (Img2.jpg). If I uncheck that box and transform, the model just reverts back to its original position after saving and reopening. I was wondering if there was a command line command for the " move atoms instead of coordinate axes " option. I have tried all the move commands ( https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/move.html) and they don't seem to work. I expect your reply soon. Sincerely, Ritwik Jain

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chimera installation problem
by Monojit roy 18 Jun '21

18 Jun '21

sir, please help

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AddH on N atom in N-terminal
by 陈恩博 17 Jun '21

17 Jun '21

Hello. When I use addH to add H atoms on N atom in N-terminal of Peptide chain, I find 3 H were added on this N. Why the addH result is C-NH3 and not C-NH2? Thanks!

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color maps based on real space cross correlation
by manikandank 16 Jun '21

16 Jun '21

Hi Chimera-users, I have aligned two cryoEM maps at certain threshold using 'Fit in Map' option in chimera. Now I would like to color one map based on real space voxel correlation values from 'Fit in Map' operation. Please let me know how this can be done in chimera. thank you with kind regards Mani.

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command line: how to add hydrogens to a phosphate group?
by Sara Luz Gomez Maya 15 Jun '21

15 Jun '21

Hi, I have a system consisting of a molecule intercalated into DNA. For a very specific application, I need to remove all the Sodium atoms from a PDB file and, in turn, add hydrogens to all the DNA phosphate groups (whatever the oxygen). Since for chimera that atom type is identified as O3- (possibly resonance-equivalent terminal oxygen on tetrahedral center (phosphate, sulfate, N-oxide), I have tried: labelopt info idatmType label #0 addh spec O3- but it did not work. You can find attached herewith the pdb file. Any help is appreciated. Regards, Sara

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Sending Chimera MD job to remote computer
by Cowie, Connor 14 Jun '21

14 Jun '21

Hello, I am using Terminal to try to run Chimera MD simulations on a remote server/computer. I have been able to successfully connect using the command ssh username@detroit05 (and then entering the password). However, I want to be able to send a command to a remote computer to improve the computational time especially when running multiple MD simulations; right now, I am running MD simulations on the same computer. I was first thinking of a sequence of commands below: Ctrl+Z bg ssh -y username@detroit05 I know that the Ctrl+Z command temporarily pauses a command, but I believe that the jobs command is first needed to list the current running jobs (that Ctrl+Z can be performed on). However, the running jobs are not listed when I type “jobs”. After using the “top” command to list all of the processes, I have verified that the Kill command works by typing these in succession: Kill -STOP PID# Kill -CONT PID# Can you walk me through how to first have a listing of jobs running in Chimera and then sending it to a remote computer? Best, Connor

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getting surface patches
by Diego Amaya 13 Jun '21

13 Jun '21

Hello all, I'm trying to get surface patches of PDB structures in VTK format. So I want to define a patch as the set of atoms within a given radius of a specific residue, build the surface corresponding to that patch and export the result in VTK format. Additionally, I want to do all this with a python script. Here the code I'm trying but doesn't work : *import pychimerapychimera.patch_environ()pychimera.enable_chimera()import osimport chimerafrom chimera import runCommand as rc* *list_resid = [31, 64]* *radius = 3list_pdbs = ['ensayo.pdb']for resid in list_resid: for line in list_pdbs: list_atoms = [] rc('open '+line) rc('sel :{} za<{}'.format(resid, radius)) for a in chimera.selection.currentAtoms(): list_atoms.append('serialNumber=' + str(a.serialNumber)) sel_atoms = ' or '.join(list_atoms) rc('surfcat patch @*/{}'.format(sel_atoms)) rc('surface patch') rc("export format VTK {}_resid_{}_radius_{}.vtk".format(line[:-4], resid, radius)) rc("close all")* Thanks in advance for your help. -- Diego A. Amaya Ramírez -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

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Minimize hydrogens in water molecules
by Francesca Magarotto - francesca.magarotto2＠studio.unibo.it 11 Jun '21

11 Jun '21

Hi, I need to minimize two water molecules in the binding site of the protein: I don't want to move the oxygen, so I've selected only hydrogen atoms and then I' ve used the Minimize Structure tool (keeping fixed all atoms that are unselected). I can't do the minimization because there's an error: Chimera/MMTK cannot minimize structure, probably because there is no parameter for ''No parameters for bond Atom 0.CYS_394__0_0_1_397__A.N (atom type n) - Atom 0.GLY_393__0_0_1_396__A.peptide.C (atom type C)'' I don't known what this means and what I should do to fix it. I've tried to use the command line, but there's another error. Does anyone have suggestions? Thank you. Francesca

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search a sequence in UCSF chimera
by Xiao Lei 10 Jun '21

10 Jun '21

Dear chimera-users, Is there a way to search a short amino acid sequence (for example: DDDDK) in an openned protein structure in UCSF chimera? Thanks ahead, Xiao

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Removing specific water molecules
by Francesca Magarotto - francesca.magarotto2＠studio.unibo.it 10 Jun '21

10 Jun '21

Hi, I have a problem using Chimera: I need to delete specific water molecules with a specific residue number, but this number is in common with residues that are useful (such as ligands or co-factors). For example, I type "del :546-893" in the command line in order to delete these water molecules, but I delete also the ligand and FAD and I don't want to. I've read the guide about atom specification, but still I don't know how to do it. Hope someone can help me, thank you. Francesca

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Re: [Chimera-users] [ChimeraX] #4232: RFE: make ViewDockX understand SwissDock output
by Elaine Meng 07 Jun '21

07 Jun '21

Hi Michael, I edited out the details of your files below in case you wanted to keep that private, but am CC-ing the chimera users list recommended for asking questions. Since the Swissdock server only keeps the files for a while, I understand you had to save them locally and now you are trying to modify the Chimera web-data files to use the local files. However, I think you can simplify and no longer use a web-data file, but simply a Chimera command file (see below), since the python stuff was just retrieving the files. In that case you would just insert the local file pathnames into the commands that open them. Just name the plain text file containing the commands something.com and open it with Chimera. The command file (plain text) would contain something like this, of course substituting your actual file locations for "[pathname-...]": open [pathname-of-pdb-file] viewdock [pathname-of-docked-ligands-file] color byatom #0 ribbon #0 repr stick :LIG ~disp element.H hbonds intramodel false lineWidth 5 color green Other than the opening of files, you wouldn't necessarily have to use those same commands, you could customize as desired. Further, you could just type in the commands into the command line one by one instead of making a command file, if that's easier. Chimera command files: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 7, 2021, at 9:04 AM, Michael Weber <weberm(a)posteo.de> wrote: > > Dear Elaine, > thank you for your quick response. > > I have a question: when now trying to use Chimera instead of ChimeraX to analyze my SwissDock output files I noted that the files may only be analyzed as long as the entire data set related to that docking experiment is still available online on the SwissDock website. Fortunately, I had downloaded the entire data sets and stored them locally. > SwissDock delivers some sort of script in which Chimera commands and the required input file locations are stored as follows: > > <?xml version="1.0"?> > <ChimeraPuppet type="std_webdata"> > <web_files> > <file name="target.pdb" format="text" loc="http://www.swissdock.ch/files/tmp/[...other stuff...]/target.pdb" /> > </web_files> > <commands> > <py_cmd> > import urllib > import tempfile > from chimera import runCommand > tmpDirectory = tempfile.mkdtemp() > urllib.urlretrieve ("http://www.swissdock.ch/files/tmp/[...other stuff...]/clusters.dock4.pdb", "%s/clusters.dock4.pdb"%tmpDirectory) > runCommand("viewdock %s/clusters.dock4.pdb \"Dock 4, 5 or 6\""%tmpDirectory) > </py_cmd> > <mid_cmd>color byatom #0</mid_cmd> > <mid_cmd>ribbon #0</mid_cmd> > <mid_cmd>repr stick :LIG</mid_cmd> > <mid_cmd>~disp element.H</mid_cmd> > <mid_cmd>hbonds intramodel false lineWidth 5 color green</mid_cmd> > </commands> > </ChimeraPuppet> > > I thought I might cure the situation by replacing the web locations by the local hard drive file locations, so I modified it as follows: > [... edited out...] > Of course it does not work properly because I don't know what exactly the syntax looks like for solving my problem when working with local files. > I hope it is not asked too much, but could you help me how to fix this? > > Best regards, > Michael.

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command line clustering (how to select a subSection?)
by Laura Morris 04 Jun '21

04 Jun '21

Recently I've been clustering in Chimera but running into memory limitations on my system. I'd like to do the clustering on a computer with more RAM, but I need to be able to do this using only the command line. I found an old post (http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-May/005166.html) that includes an example script to do the clustering, but I don't know how to change the subSection to the residues and atoms I want. Here's the portion of relevant code: def main(): import chimera modelList = chimera.openModels.list(modelTypes=[chimera.Molecule]) subSelection = None # Change this to CAs or heavy atoms clusterInfo = _cluster(modelList, subSelection) saveReps(clusterInfo, "reps.pdb") # Change file name if needed The "Change this to CAs or heavy atoms" is exactly what I want to do, but I have no idea how to do it. If this were command line in Chimera, I'd use something like "select #0:3-55@CA". I know there's a "runCommand" function that can be included (using "from chimera import runCommand"). Is this used in some way to set subSelection, and if so, how? Any help is appreciated. Regards, Laura ----- Laura C. Morris Scientific Computing Professional Edison & Prestegard Labs Complex Carbohydrate Research Center 706-542-6286 (lab 1075)

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command question
by Yanhe Zhao 01 Jun '21

01 Jun '21

Good afternoon Elaine and users, I have two questions as to Chimera using as below: 1, how can I plane through and rotate volume at same time? For example how to add rotate options to command "volume #2 planes x,0,42,1; wait 43;"? 2, How I can merge volumes (for example 3 volumes) with their own threshold was kept? Thanks and best, Yanhe

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saving segmented copy of a map
by M.S. Islam 01 Jun '21

01 Jun '21

Hi I was just wondering, is there any way that I can save segmented copy of a map so that I don't have to do segmentation, followed by colouring different segments of the segmented map again and again. Thanks a lot in advance. Saif

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Fwd: Cannot see menus on MacBook Mojave
by Elaine Meng 01 Jun '21

01 Jun '21

> Begin forwarded message: > > From: Eric Werner <evwerner(a)gmail.com> > Subject: Cannot see menus on MacBook Mojave > Date: May 24, 2021 at 9:10:48 PM PDT > > Hi, > > Chimera is great. However in the latest download for the Mac, I can no longer see the menus when in Dark Mode on my Macbook Pro using Mojave. > > In the attached file you can see the the transparent background of the menu drop down list makes it even harder. > > Is there a solution to adjust the menu text and background color and making the menu background opaque? > > Thank you for your help. > > Eric >

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Structure to sequence alignment
by Kamil Steczkiewicz 31 May '21

31 May '21

Dear Chimera community, Does Chimera allow to display multiple protein structures as CA trace, colour corresponding residues in 3d, display these proteins' sequences in alignment window and allow to manually alter the alignment to manually align residues coloured as mutually corresponding (preferably by mouse)? Something like was possible in good old and unfortunately not supported any more Insight program... That's what wraps up to so-called structure-based manual multiple sequence alignment. Essential if you're assessing some highly diversified set of structures and want to have a precise alignment for them. Thanks, Kamil *Kamil Steczkiewicz, PhD* Department of Bioinformatics Institute of Biochemistry and Biophysics Polish Academy of Sciences tel. +48 22 592 *5759 *| +48 668 13 02 13

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Getting the median protein structure after comparing.
by Shradheya R.R. Gupta 29 May '21

29 May '21

Hi, I have two PDB's I compared (superimposed) them using the Chimera tool. But some regions are not superimposed. I want to generate the new PDB which have the superimposed regions coordinates and the median coordinates of the region which is not superimposed. Thank you

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Help needed
by Nirban Dey 28 May '21

28 May '21

Hello, I am a Masters student in India currently using chimera for my thesis. I am facing a problem. I have attached a state file of my docked complex. There some residues 251, 245, 243 formed H bonds with the ligand through the O atom. I am not able to display the residue clearly. O atom is looking like a dot. I want to show the residue clearly making bonds with the ligand without hiding the ribbon like the residue 247. Those residues are clearly visible only if I hide ribbons for that residue. Kindly help me to show the residue properly without hiding their ribbon. Regards Nirban

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Quantify the movement between two domains
by Ahmad Khalifa 27 May '21

27 May '21

Hi, I'm looking for a way to quantify the movement between two domains in my structure. I know I can calculate an RMSD between the same domains in different conformations. I can also generate a distance matrix between the two chains in different conformations. I tried to measure the distance between the two centers of mass of my domains, but the change doesn't really capture the magnitude of the movement, also the same domains are not identical in the two conformations in the sense that one domain is missing so many loops, which will affect the com calculation. What other ways to quantify the distance between two different domains? Thank you.

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